extend XML model for graduated feature colours, group associated manual/auto annotati...

[jalview.git] / src / jalview / schemabinding / version2 / Annotation.java

diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java
index 1649f20..b7056c4 100755 (executable)
--- a/src/jalview/schemabinding/version2/Annotation.java
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -63,6 +63,11 @@ public class Annotation implements java.io.Serializable {
     private java.lang.String _sequenceRef;\r
 \r
     /**\r
+     * Field _groupRef.\r
+     */\r
+    private java.lang.String _groupRef;\r
+\r
+    /**\r
      * Field _graphColour.\r
      */\r
     private int _graphColour;\r
@@ -118,6 +123,46 @@ public class Annotation implements java.io.Serializable {
     private boolean _has_visible;\r
 \r
     /**\r
+     * Field _centreColLabels.\r
+     */\r
+    private boolean _centreColLabels;\r
+\r
+    /**\r
+     * keeps track of state for field: _centreColLabels\r
+     */\r
+    private boolean _has_centreColLabels;\r
+\r
+    /**\r
+     * Field _scaleColLabels.\r
+     */\r
+    private boolean _scaleColLabels;\r
+\r
+    /**\r
+     * keeps track of state for field: _scaleColLabels\r
+     */\r
+    private boolean _has_scaleColLabels;\r
+\r
+    /**\r
+     * Field _showAllColLabels.\r
+     */\r
+    private boolean _showAllColLabels;\r
+\r
+    /**\r
+     * keeps track of state for field: _showAllColLabels\r
+     */\r
+    private boolean _has_showAllColLabels;\r
+\r
+    /**\r
+     * is an autocalculated annotation row\r
+     */\r
+    private boolean _autoCalculated = false;\r
+\r
+    /**\r
+     * keeps track of state for field: _autoCalculated\r
+     */\r
+    private boolean _has_autoCalculated;\r
+\r
+    /**\r
      * Field _annotationElementList.\r
      */\r
     private java.util.Vector _annotationElementList;\r
@@ -182,6 +227,20 @@ public class Annotation implements java.io.Serializable {
 \r
     /**\r
      */\r
+    public void deleteAutoCalculated(\r
+    ) {\r
+        this._has_autoCalculated= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteCentreColLabels(\r
+    ) {\r
+        this._has_centreColLabels= false;\r
+    }\r
+\r
+    /**\r
+     */\r
     public void deleteGraph(\r
     ) {\r
         this._has_graph= false;\r
@@ -210,6 +269,13 @@ public class Annotation implements java.io.Serializable {
 \r
     /**\r
      */\r
+    public void deleteScaleColLabels(\r
+    ) {\r
+        this._has_scaleColLabels= false;\r
+    }\r
+\r
+    /**\r
+     */\r
     public void deleteScore(\r
     ) {\r
         this._has_score= false;\r
@@ -224,6 +290,13 @@ public class Annotation implements java.io.Serializable {
 \r
     /**\r
      */\r
+    public void deleteShowAllColLabels(\r
+    ) {\r
+        this._has_showAllColLabels= false;\r
+    }\r
+\r
+    /**\r
+     */\r
     public void deleteVisible(\r
     ) {\r
         this._has_visible= false;\r
@@ -288,6 +361,28 @@ public class Annotation implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'autoCalculated'. The field\r
+     * 'autoCalculated' has the following description: is an\r
+     * autocalculated annotation row\r
+     * \r
+     * @return the value of field 'AutoCalculated'.\r
+     */\r
+    public boolean getAutoCalculated(\r
+    ) {\r
+        return this._autoCalculated;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'centreColLabels'.\r
+     * \r
+     * @return the value of field 'CentreColLabels'.\r
+     */\r
+    public boolean getCentreColLabels(\r
+    ) {\r
+        return this._centreColLabels;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'description'.\r
      * \r
      * @return the value of field 'Description'.\r
@@ -338,6 +433,16 @@ public class Annotation implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'groupRef'.\r
+     * \r
+     * @return the value of field 'GroupRef'.\r
+     */\r
+    public java.lang.String getGroupRef(\r
+    ) {\r
+        return this._groupRef;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'id'.\r
      * \r
      * @return the value of field 'Id'.\r
@@ -358,6 +463,16 @@ public class Annotation implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'scaleColLabels'.\r
+     * \r
+     * @return the value of field 'ScaleColLabels'.\r
+     */\r
+    public boolean getScaleColLabels(\r
+    ) {\r
+        return this._scaleColLabels;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'score'.\r
      * \r
      * @return the value of field 'Score'.\r
@@ -388,6 +503,16 @@ public class Annotation implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showAllColLabels'.\r
+     * \r
+     * @return the value of field 'ShowAllColLabels'.\r
+     */\r
+    public boolean getShowAllColLabels(\r
+    ) {\r
+        return this._showAllColLabels;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'thresholdLine'.\r
      * \r
      * @return the value of field 'ThresholdLine'.\r
@@ -408,6 +533,26 @@ public class Annotation implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Method hasAutoCalculated.\r
+     * \r
+     * @return true if at least one AutoCalculated has been added\r
+     */\r
+    public boolean hasAutoCalculated(\r
+    ) {\r
+        return this._has_autoCalculated;\r
+    }\r
+\r
+    /**\r
+     * Method hasCentreColLabels.\r
+     * \r
+     * @return true if at least one CentreColLabels has been added\r
+     */\r
+    public boolean hasCentreColLabels(\r
+    ) {\r
+        return this._has_centreColLabels;\r
+    }\r
+\r
+    /**\r
      * Method hasGraph.\r
      * \r
      * @return true if at least one Graph has been added\r
@@ -448,6 +593,16 @@ public class Annotation implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Method hasScaleColLabels.\r
+     * \r
+     * @return true if at least one ScaleColLabels has been added\r
+     */\r
+    public boolean hasScaleColLabels(\r
+    ) {\r
+        return this._has_scaleColLabels;\r
+    }\r
+\r
+    /**\r
      * Method hasScore.\r
      * \r
      * @return true if at least one Score has been added\r
@@ -468,6 +623,16 @@ public class Annotation implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Method hasShowAllColLabels.\r
+     * \r
+     * @return true if at least one ShowAllColLabels has been added\r
+     */\r
+    public boolean hasShowAllColLabels(\r
+    ) {\r
+        return this._has_showAllColLabels;\r
+    }\r
+\r
+    /**\r
      * Method hasVisible.\r
      * \r
      * @return true if at least one Visible has been added\r
@@ -478,6 +643,28 @@ public class Annotation implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'autoCalculated'. The field\r
+     * 'autoCalculated' has the following description: is an\r
+     * autocalculated annotation row\r
+     * \r
+     * @return the value of field 'AutoCalculated'.\r
+     */\r
+    public boolean isAutoCalculated(\r
+    ) {\r
+        return this._autoCalculated;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'centreColLabels'.\r
+     * \r
+     * @return the value of field 'CentreColLabels'.\r
+     */\r
+    public boolean isCentreColLabels(\r
+    ) {\r
+        return this._centreColLabels;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'graph'.\r
      * \r
      * @return the value of field 'Graph'.\r
@@ -488,6 +675,16 @@ public class Annotation implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'scaleColLabels'.\r
+     * \r
+     * @return the value of field 'ScaleColLabels'.\r
+     */\r
+    public boolean isScaleColLabels(\r
+    ) {\r
+        return this._scaleColLabels;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'scoreOnly'.\r
      * \r
      * @return the value of field 'ScoreOnly'.\r
@@ -498,6 +695,16 @@ public class Annotation implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showAllColLabels'.\r
+     * \r
+     * @return the value of field 'ShowAllColLabels'.\r
+     */\r
+    public boolean isShowAllColLabels(\r
+    ) {\r
+        return this._showAllColLabels;\r
+    }\r
+\r
+    /**\r
      * Method isValid.\r
      * \r
      * @return true if this object is valid according to the schema\r
@@ -621,6 +828,30 @@ public class Annotation implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'autoCalculated'. The field\r
+     * 'autoCalculated' has the following description: is an\r
+     * autocalculated annotation row\r
+     * \r
+     * @param autoCalculated the value of field 'autoCalculated'.\r
+     */\r
+    public void setAutoCalculated(\r
+            final boolean autoCalculated) {\r
+        this._autoCalculated = autoCalculated;\r
+        this._has_autoCalculated = true;\r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'centreColLabels'.\r
+     * \r
+     * @param centreColLabels the value of field 'centreColLabels'.\r
+     */\r
+    public void setCentreColLabels(\r
+            final boolean centreColLabels) {\r
+        this._centreColLabels = centreColLabels;\r
+        this._has_centreColLabels = true;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'description'.\r
      * \r
      * @param description the value of field 'description'.\r
@@ -675,6 +906,16 @@ public class Annotation implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'groupRef'.\r
+     * \r
+     * @param groupRef the value of field 'groupRef'.\r
+     */\r
+    public void setGroupRef(\r
+            final java.lang.String groupRef) {\r
+        this._groupRef = groupRef;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'id'.\r
      * \r
      * @param id the value of field 'id'.\r
@@ -695,6 +936,17 @@ public class Annotation implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'scaleColLabels'.\r
+     * \r
+     * @param scaleColLabels the value of field 'scaleColLabels'.\r
+     */\r
+    public void setScaleColLabels(\r
+            final boolean scaleColLabels) {\r
+        this._scaleColLabels = scaleColLabels;\r
+        this._has_scaleColLabels = true;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'score'.\r
      * \r
      * @param score the value of field 'score'.\r
@@ -727,6 +979,17 @@ public class Annotation implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'showAllColLabels'.\r
+     * \r
+     * @param showAllColLabels the value of field 'showAllColLabels'\r
+     */\r
+    public void setShowAllColLabels(\r
+            final boolean showAllColLabels) {\r
+        this._showAllColLabels = showAllColLabels;\r
+        this._has_showAllColLabels = true;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'thresholdLine'.\r
      * \r
      * @param thresholdLine the value of field 'thresholdLine'.\r